RandAffined does not work as expected

[Spenhouet]

Describe the bug

Given the following image and label:

When applying RandAffined, the image and labels no longer match:

To Reproduce

Steps to reproduce the behavior:

1. Load these files: example_files.zip
2. Execute this pipeline:

from pathlib import Path

import numpy as np
from monai.transforms.compose import Compose
from monai.transforms.io.dictionary import LoadImaged, SaveImaged
from monai.transforms.spatial.dictionary import RandAffined
from monai.transforms.utility.dictionary import (EnsureChannelFirstd, ToTensord)
from monai.utils.enums import GridSampleMode

path = Path('scratch/rand_affine')

T1_KEY = 't1'
LABEL_KEY = 'labels'
FILE_KEYS = [T1_KEY, LABEL_KEY]
SAMPLE_MODES = [GridSampleMode.BILINEAR, GridSampleMode.NEAREST]

data = {
    T1_KEY: path / 't1.nii.gz',
    LABEL_KEY: path / 'labels.nii.gz',
}

process = Compose([
    LoadImaged(FILE_KEYS),
    ToTensord(FILE_KEYS),
    EnsureChannelFirstd(FILE_KEYS),
    RandAffined(
        FILE_KEYS,
        rotate_range=5.0 * np.pi / 180.0,  # type: ignore
        prob=1.0,
        mode=SAMPLE_MODES,
        allow_missing_keys=True,
    ),
    SaveImaged(
        FILE_KEYS,
        output_dir=path,
        output_postfix=f"out",
        resample=False,
        output_dtype=np.float32,
        separate_folder=False,
        print_log=False,
    )
])

process([data])

Expected behavior
The same random affine transformation is applied to all images.
After the transform the labels still match the image.

Additional context
I did not yet identify the issue.

[wyli]

I couldn't replicate the issue locally with a macbook and visualise with itk-snap.

could you help provide more info?

[Spenhouet]

@wyli You did not use the data provided by me. Could you try it with that? It is part of the reproduction.

[wyli]

@wyli You did not use the data provided by me. Could you try it with that? It is part of the reproduction.

I downloaded and unzipped the file, there are two files, t1.nii.gz and labels.nii.gz. itk-snap refuses to display

the labels.nii.gz as segmentations for t1.nii.gz

[Spenhouet]

I'm not a itk-snap user but if there is a problem in itk-snap probably good to report it to their project. Not really the issue I'm reporting here though.

Try using MRIcroGL or Slicer. Both work fine.